2W8L

Y-FAMILY DNA POLYMERASE DPO4 BYPASSING N2-NAPHTHYL-GUANINE ADDUCT IN ANTI ORIENTATION

Structural Biology Knowledgebase: 2W8L SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.282
  • R-Value Work: 0.226

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2W8L

Classification: TRANSFERASE / DNA

Total Structure Weight: 51549.90


Macromolecule Entities
Molecule Chains Length Organism Details
DNA POLYMERASE IV A 358 Sulfolobus solfataricus EC#: 2.7.7.7 IUBMB
Details: Y-FAMILY DNA POLYMERASE FROM SULFOLOBUS SOLFATARICUS
Gene Name(s): dbh dpo4 SSO2448
Macromolecule Entities
Molecule Chains Length Organism Details
5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *TP*TP*CP*DOC)-3' P 14 synthetic 14 BASE PRIMER DNA 5'-GGG GGA AGG ATT CC-3'
5'-D(*TP*CP*AP*CP*N2GP*GP*AP*AP*TP*CP *CP*TP*TP*CP*CP*CP*CP*C)-3' T 18 synthetic 18 BASE TEMPLATE DNA 5'-TCA C(NPG)G AAT CCT TCC CCC-3'

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
DGT
Query on DGT

A 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
HAAZLUGHYHWQIW-KVQBGUIXSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
DGT N/A in BindingDB
N/A in BindingMoad
Kd: 29000 nM  PDBbind
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
DOC
Query on DOC
P DNA LINKING C9 H14 N3 O6 P DC
N2G
Query on N2G
T non-polymer C21 H22 N5 O7 P --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.282
  • R-Value Work: 0.226
  • Space Group: P 21 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 95.92 α = 90.00
b = 103.83 β = 90.00
c = 52.49 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-01-16
  • Released Date: 2009-01-27
  • Deposition author(s): Eoff, R.L., Zhang, H., Egli, M., Guengerich, F.P.
  • Previous versions: 2V4T

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4